Fluid processing and control

ABSTRACT

A fluid control and processing system for controlling fluid flow among a plurality of chambers comprises a body including a fluid processing region continuously coupled fluidicly with a fluid displacement region. The fluid displacement region is depressurizable to draw fluid into the fluid displacement region and pressurizable to expel fluid from the fluid displacement region. The body includes at least one external port. The fluid processing region is fluidicly coupled with the at least one external port. The fluid displacement region is fluidicly coupled with at least one external port of the body. The body is adjustable with respect to the plurality of chambers to place the at least one external port selectively in fluidic communication with the plurality of chambers. One or more of the chambers may be a processing chamber which includes two ports configured to selectively engage the at least one external port of the body, and a fluid processing material such as an enrichment material or a depletion material. In some embodiments, one or more chambers may include a separation channel, and an electric field may be applied across the separation channel.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.14/169,402, filed Jan. 31, 2014, which is a continuation of U.S. patentapplication Ser. No. 13/854,297, filed Apr. 1, 2013, now U.S. Pat. No.8,673,238, which is a divisional of U.S. patent application Ser. No.13/245,572 filed Sep. 26, 2011, now U.S. Pat. No. 8,431,413, which is adivisional of U.S. patent application Ser. No. 10/084,409, filed Feb.25, 2002, now U.S. Pat. No. 8,048,386 and is related to commonlyassigned U.S. patent application Ser. No. 09/648,570, filed Aug. 25,2000, now U.S. Pat. No. 6,374,684, the entire disclosure of all of theabove is incorporated herein by reference.

BACKGROUND OF THE INVENTION

The present invention relates generally to fluid manipulation and, moreparticularly, to a system and method for metering and distributing fluidfor processing and analysis.

The analysis of fluids such as clinical or environmental fluidsgenerally involves a series of processing steps, which may includechemical, optical, electrical, mechanical, thermal, or acousticalprocessing of the fluid samples. Whether incorporated into a bench-topinstrument, a disposable cartridge, or a combination of the two, suchprocessing typically involves complex fluidic assemblies and processingalgorithms.

Conventional systems for processing fluid samples employ a series ofchambers each configured for subjecting the fluid sample to a specificprocessing step. As the fluid sample flows through the systemsequentially from chamber to chamber, the fluid sample undergoes theprocessing steps according to a specific protocol. Because differentprotocols require different configurations, conventional systemsemploying such sequential processing arrangements are not versatile oreasily adaptable to different protocols.

SUMMARY OF THE INVENTION

The present invention provides an apparatus and method for manipulatingfluids, for instance, to determine the presence or absence of an analytein a sample. In a specific embodiment, the apparatus employs a rotaryvalve configuration that allows fluidic communication between a fluidprocessing region selectively with a plurality of chambers including,for example, a sample chamber, a waste chamber, a wash chamber, a lysischamber, and a mastermix or reagent chamber. The fluid flow among thefluid processing region and the chambers is controlled by adjusting theposition of the rotary valve. In this way, the metering and distributionof fluids in the apparatus can be varied depending on the specificprotocol. Unlike conventional devices, the fluid flow is no longerlimited to a specific protocol.

In accordance with an aspect of the present invention, a fluid controland processing system comprises a housing having a plurality ofchambers, and a valve body including a first fluid processing regioncontinuously coupled fluidicly with a fluid displacement region. Thefluid displacement region is depressurizable to draw fluid into thefluid displacement region and pressurizable to expel fluid from thefluid displacement region. The valve body includes a plurality ofexternal ports. The first fluid processing region is fluidicly coupledwith at least two of the external ports. The fluid displacement regionis fluidicly coupled with at least one of the external ports of thevalve body. The valve body is adjustable with respect to the housing toallow the external ports to be placed selectively in fluidiccommunication with the plurality of chambers. At least one of theplurality of chambers is a processing chamber including a first port anda second port for selectively communicating with at least one of theexternal ports of the valve body. The processing chamber provides anadditional fluid processing region.

In some embodiments, at least one of the fluid processing regions in thevalve body or in the processing chamber contains a fluid processingmaterial which is an enrichment material or a depletion material. Thefluid processing material may comprise at least one solid phasematerial. The solid phase material may comprise at least one of beads,fibers, membranes, filter paper, glass wool, polymers, and gels. Thefluid processing material may comprise a filter and beads, or at leasttwo types of beads. In a specific embodiments, a single type of beads isused to perform at least two different functions which are selected fromthe group consisting of cell capture, cell lysis, binding of analyte,and binding of unwanted material. In some embodiments, the processingchamber includes a receiving area for receiving a processing modulecontaining an enrichment material or a depletion material. In a specificembodiment, at least one of the chambers is a reagent chamber containingdried or lyophilized reagents.

In some embodiments, the fluid processing material comprises at leastone liquid phase material, such as ficoll, dextran, polyethylene glycol,and sucrose. The fluid processing material is contained in the fluidprocessing region by one or more frits. In a specific embodiment, theexternal ports are disposed on a generally planar external port surfaceof the valve body.

In accordance with another aspect of the invention, a fluid control andprocessing system comprises a housing having a plurality of chambers andat least one separation channel (e.g., for performing capillaryelectrophoresis or isoelectric focusing), and a valve body including afluid processing region continuously coupled fluidicly with a fluiddisplacement region. The fluid displacement region is depressurizable todraw fluid into the fluid displacement region and pressurizable to expelfluid from the fluid displacement region. The valve body includes atleast one external port, the fluid processing region is fluidiclycoupled with the at least one external port, and the fluid displacementregion is fluidicly coupled with at least one external port of the valvebody. The valve body is adjustable with respect to the housing to allowthe at least one external port to be placed selectively in fluidiccommunication with the plurality of chambers and with the at least oneseparation channel.

In some embodiments, a plurality of electrodes are coupled to thehousing to apply an electric field across at least a portion of theseparation channel. The electrodes preferably comprise a pair of metaltubes at the two opposite ends of the separation channel. Reservoirs areprovided at both ends of the separation channel, and a reservoir port isprovided at one of the reservoirs for communicating with the at leastone external port of the valve body.

Another aspect of the present invention is directed to a method forcontrolling fluid flow between a valve, a plurality of chambers, and atleast one separation channel, wherein the valve includes at least oneexternal port and a fluid displacement region continuously coupledfluidicly with a fluid processing region which is fluidicly coupled withthe at least one external port. The method comprises adjusting the valvewith respect to the plurality of chambers and the at least oneseparation channel to place the at least one external port selectivelyin fluidic communication with the plurality of chambers and the at leastone separation channel.

In some embodiments, an electric field is applied across at least aportion of the separation channel. The method may comprise opticallydetecting species bands in the separation channel.

In accordance with another aspect of the invention, a fluid control andprocessing system comprises a housing having a plurality of chambers,and a valve body including a fluid processing region continuouslycoupled fluidicly with a fluid displacement region. The fluiddisplacement region is depressurizable to draw fluid into the fluiddisplacement region and pressurizable to expel fluid from the fluiddisplacement region. The valve body includes an external port. The fluidprocessing region is fluidicly coupled with the external port. The fluiddisplacement region is fluidicly coupled with the external port of thevalve body. The valve body is adjustable with respect to the housing toallow the external port to be placed selectively in fluidiccommunication with the plurality of chambers.

In some embodiments, the valve body is adjustable with respect to thehousing to close the external port so that the fluid displacement regionand the fluid processing region are fluidicly isolated from thechambers. At least one of the chambers and the fluid processing regionmay contain an enrichment material or a depletion material. The fluiddisplacement region is depressurizable by increasing in volume and ispressurizable by decreasing in volume. A fluid displacement member isdisposed in the fluid displacement region, and is movable to adjust thevolume of the fluid displacement region. An energy transmitting memberis operatively coupled with the fluid processing region for transmittingenergy thereto to process fluid contained therein.

In specific embodiments, the valve body includes a crossover channel.The valve body is adjustable with respect to the housing to place thecrossover channel in fluidic communication with an aspiration chamberand a source chamber to permit aspiration of a fluid from the sourcechamber through the crossover channel to the aspiration chamber. Thebody is rotatably adjustable around an axis. The at least one externalport is disposed within a range of external port radii from the axis andthe crossover channel is disposed within a range of crossover channelradii from the axis. The range of external port radii and the range ofcrossover channel radii are non-overlapping. The crossover channel maybe a circular arc lying on a common crossover channel radius from theaxis.

In accordance with another aspect of the present invention, a fluidcontrol and processing system for controlling fluid flow among aplurality of chambers comprises a body including a fluid processingregion continuously coupled fluidicly with a fluid displacement region.The fluid displacement region is depressurizable to draw fluid into thefluid displacement region and pressurizable to expel fluid from thefluid displacement region, the body including at least one externalport. The fluid processing region is fluidicly coupled with the at leastone external port. The fluid displacement region is fluidicly coupledwith at least one external port of the valve body. The body is rotatablyadjustable and relative to the plurality of chambers to place the atleast one external port selectively in fluidic communication with theplurality of chambers.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a perspective view of the fluid control and processing systemaccording to an embodiment of the present invention;

FIG. 2 is another perspective view of the system of FIG. 1;

FIG. 3 is an exploded view of the system of FIG. 1;

FIG. 4 is an exploded view of the system of FIG. 2;

FIG. 5 is an elevational view of a fluid control apparatus and gasket inthe system of FIG. 1;

FIG. 6 is a bottom plan view of the fluid control apparatus and gasketof FIG. 5;

FIG. 7 is a top plan view of the fluid control apparatus and gasket ofFIG. 5;

FIG. 8 is a cross-sectional view of the rotary fluid control apparatusof FIG. 7 along 8-8;

FIGS. 9A-9LL are top plan views and cross-sectional views illustrating aspecific protocol for controlling and processing fluid using the fluidcontrol and processing system of FIG. 1;

FIG. 10 is an exploded perspective view of the fluid control andprocessing system according to another embodiment of the presentinvention;

FIG. 11 is a cross-sectional view of a fluid control apparatus in thesystem of FIG. 10;

FIGS. 12A-12N are plan views illustrating a specific protocol forcontrolling and processing fluid using the fluid control and processingsystem of FIG. 10;

FIG. 13 is a cross-sectional view of a soft-walled chamber;

FIG. 14 is a cross-sectional view of a piston assembly;

FIG. 15 is a cross-sectional view of a side filtering chamber;

FIG. 16 is a top plan view of a fluid control and processing systemincluding a processing chamber according to another embodiment of thepresent invention;

FIG. 17 is a perspective view of the processing chamber of FIG. 16;

FIG. 18 is a partially cut-out, sectional view of the fluid control andprocessing system of FIG. 16;

FIG. 19 is a sectional perspective view of the processing chamber ofFIG. 16

FIG. 20 is a perspective view of a retaining member of the processingchamber of FIG. 16;

FIG. 21 is an elevational view of the retaining member of FIG. 20;

FIG. 22 is a top plan view of the retaining member of FIG. 20;

FIG. 23 is a cross-sectional view of the retaining member along 23-23 ofFIG. 22;

FIG. 24 is a sectional view of a fluid control and processing systemincluding a separation channel according to another embodiment of thepresent invention;

FIG. 25 is a cross-sectional view of a fluid control apparatus in afluid control and processing system according to another embodiment ofthe present invention; and

FIGS. 26A-26EE are top plan views and cross-sectional views illustratinga specific protocol for controlling and processing fluid using the fluidcontrol and processing system of FIG. 25.

DESCRIPTION OF THE SPECIFIC EMBODIMENTS

FIGS. 1-4 show a fluid control and processing system 10 including ahousing 12 having a plurality of chambers 13. FIG. 1 shows the chambers13 exposed for illustrative purposes. A top cover will typically beprovided to enclose the chambers 13. As best seen in FIGS. 3 and 4, afluid control device 16 and a reaction vessel 18 are connected todifferent portions of the housing 12. The fluid control device in theembodiment shown is a rotary fluid control valve 16. The valve 16includes a valve body 20 having a disk portion 22 and a tubular portion24. The disk portion 22 has a generally planar external port surface 23,as best seen in FIG. 3. The valve 16 is rotatable relative to thehousing 12. The housing 12 includes a plurality of chamber ports 25facing the external port surface 23 of the disk portion 22 of the valve16 (FIG. 4) to permit fluidic communication between the chambers 13 andthe valve 16. An optional seal or gasket 26 is disposed between the diskportion 22 and the housing 12. The disk portion 22 further includes afilter or a filter stack 27 and an outer cover 28, and a toothedperiphery 29. The cover 28 may be a rigid shell or a flexible film.

As best seen in FIG. 4, the disk portion 22 includes a fluid processingregion 30. As used herein, the term “fluid processing region” refers toa region in which a fluid is subject to processing including, withoutlimitation, chemical, optical, electrical, mechanical, thermal, oracoustical processing. For example, chemical processing may include acatalyst; optical processing may include U.V. activation; electricalprocessing may include electroporation or electrophoresis or isoelectricfocusing; mechanical processing may include mixing, filtering,pressurization, and cell disruption; thermal processing may includeheating or cooling; and acoustical processing may include the use ofultrasound. The fluid processing region may include an active member,such as the filter 27, to facilitate processing of the fluid. Examplesof active members include a microfluidic chip, a solid phase material, afilter or a filter stack, an affinity matrix, a magnetic separationmatrix, a size exclusion column, a capillary tube, or the like. Suitablesolid phase materials include, without limitation, beads, fibers,membranes, filter paper, lysis paper impregnated with a lysing agent,glass wool, polymers, or gels. In a specific embodiment, the fluidprocessing region is used to prepare a sample for further processing,for instance, in the reaction vessel 18.

As shown in FIGS. 5-8, the outer cover 28 encloses the fluid processingregion 30 and the bottom end of the disk portion 22 of the valve 16. InFIG. 8, the processing region 30 includes a first fluid processing port32 coupled to a first fluid processing channel 34, and a second fluidprocessing port 36 coupled to a second fluid processing channel 38. Thefirst fluid processing channel 34 is coupled to a first outer conduit 40ending at a first external port 42 at the external port surface 23,while the second fluid processing channel 38 is coupled to a secondouter conduit 44 ending at a second external port 46 at the externalport surface 23. A fluid displacement channel 48 is coupled to the firstfluid processing channel 34 and first conduit 40 near one end, and to afluid displacement region 50 at the other end. The first outer conduit40 serves as a common conduit for allowing fluidic communication betweenthe first external port 42 and either or both of the first fluidprocessing channel 34 and the fluid displacement channel 48. Theprocessing region 30 is in continuous fluidic communication with thefluid displacement region 50.

As shown in FIGS. 6-8, the external ports 42, 46 are angularly spacedfrom one another relative to the axis 52 of the valve 16 by about 180°.The external ports 42, 46 are spaced radially by the same distance fromthe axis 52. The axis 52 is perpendicular to the external port surface23. In another embodiment, the angular spacing between the externalports 42, 46 may be different. The configuration of the channels in thedisk portion 22 may also be different in another embodiment. Forexample, the first fluid processing channel 34 and the first outerconduit 40 may be slanted and coupled directly with the fluiddisplacement region 50, thereby eliminating the fluid displacementchannel 48. The second fluid displacement channel 38 may also be slantedand extend between the second fluid processing port 36 and the secondexternal port 46 via a straight line, thereby eliminating the secondouter conduit 44. In addition, more channels and external ports may beprovided in the valve 16. As best seen in FIG. 3, a crossover channel orgroove 56 is desirably provided on the external port surface 23. Thegroove 56 is curved and desirably is spaced from the axis 52 by aconstant radius. In one embodiment, the groove 56 is a circular arclying on a common radius from the axis 52. As discussed in more detailbelow, the groove 56 is used for filling the vessel.

As shown in FIG. 8, the fluid displacement region 50 is disposedsubstantially within the tubular portion 24 of the valve 16 and extendspartially into the disk portion 22. In a preferred embodiment, the fluiddisplacement region 50 is a pumping channel or chamber. A fluiddisplacement member in the form of a plunger or piston 54 is movablydisposed in the pumping chamber 50. When the piston 54 moves upward, itexpands the volume of the pumping chamber 50 to produce a suction fordrawing fluid into the pumping chamber 50. When the piston 54 movesdownward, it decreases the volume of the pumping chamber 50 to drivefluid out of the chamber 50. Alternatively, for example, pressurizationand depressurization of the displacement region 50 may be carried outusing a diaphragm, an external pneumatic or pressure control system, orthe like.

As the rotary valve 16 is rotated around its axis 52 relative to thehousing 12 of FIGS. 1-4, one of the external ports 42, 46 may be openand fluidicly coupled with one of the chambers 13 or reaction vessel 18,or both external ports 42, 46 may be blocked or closed. In thisembodiment, at most only one of the external ports 42, 46 is fluidiclycoupled with one of the chambers or reaction vessel 18. Otherembodiments may be configured to permit both external ports 42, 46 to befluidicly coupled with separate chambers or the reaction vessel 18.Thus, the valve 16 is rotatable with respect to the housing 12 to allowthe external ports 42, 46 to be placed selectively in fluidiccommunication with a plurality of chambers which include the chambers 13and the reaction vessel 18. Depending on which external port 42, 46 isopened or closed and whether the piston 54 is moved upward or downward,the fluid flow in the valve 16 can change directions, the external ports42, 46 can each switch from being an inlet port to an outlet port, andthe fluid flow may pass through the processing region 30 or bypass theprocessing region 30. In a specific embodiment, the first external port42 is the inlet port so that the inlet side of the processing region 30is closer to the fluid displacement region 50 than the outlet side ofthe processing region 30.

To demonstrate the fluid metering and distribution function of the valve16, FIGS. 9A-9LL illustrate the operation of the valve 16 for a specificprotocol. In FIGS. 9A and 9AA, the first external port 42 is placed influidic communication with a sample chamber 60 by rotating the valve 16,and the piston 54 is pulled upward to draw a fluid sample from thesample chamber 60 through the first outer conduit 40 and fluiddisplacement channel 48 to the fluid displacement region 50, bypassingthe processing region 30. For simplicity, the piston 54 is not shown inFIGS. 9A-9LL. The valve 16 is then rotated to place the second externalport 46 in fluidic communication with a waste chamber 64 as shown inFIGS. 9B and 9BB. The piston 54 is pushed downward to drive the fluidsample through the fluid processing region 30 to the waste chamber 64.In a specific embodiment, the fluid processing region 30 includes afilter or a filter stack 27 for capturing sample components (e.g.,cells, spores, microorganisms, viruses, proteins, or the like) from thefluid sample as it passes therethrough. An example of a filter stack isdescribed in commonly assigned, copending U.S. patent application Ser.No. 09/584,327, entitled “Apparatus and Method for Cell Disruption,”filed May 30, 2000, which is incorporated herein by reference in itsentirety. In alternative embodiments, other active members may beprovided in the processing region 30. These first two steps of capturingsample components may be repeated as desired.

In FIGS. 9C and 9CC, the valve 16 is rotated to place the first externalport 42 in fluidic communication with a wash chamber 66, and the piston54 is pulled upward to draw a wash fluid from the wash chamber 66 intothe fluid displacement region 50, bypassing the processing region 30.The valve 16 is then rotated to place the second external port 46 influidic communication with the waste chamber 64 as shown in FIGS. 9D and9DD. The piston 54 is pushed downward to drive the wash fluid throughthe fluid processing region 30 to the waste chamber 64. The abovewashing steps may be repeated as desired. The intermediate washing isused to remove unwanted residue within the valve 16.

In FIGS. 9E and 9EE, the valve 16 is rotated to place the first externalport 42 in fluidic communication with a lysis chamber 70, and the piston54 is pulled upward to draw a lysing fluid (e.g., a lysing reagent orbuffer) from the lysis chamber 70 into the fluid displacement region 50,bypassing the processing region 30. The valve 16 is then rotated toplace the second external port 46 in fluidic communication with thewaste chamber 64 as shown in FIGS. 9F and 9FF. The piston 54 is pusheddownward to drive the lysing fluid through the fluid processing region30 to the waste chamber 64. In FIGS. 9G, and 9GG, the valve 16 isrotated to close the external ports 42, 46. The piston 54 is pusheddownward to pressurize the remaining lysing fluid and the samplecomponents captured in the fluid processing region 30. Additional energymay be applied to the mixture in the processing region 30. For instance,a sonic member 76 such as an ultrasonic horn may be placed in contactwith the outer cover 28 to transmit sonic energy into the processingregion 30 to facilitate lysing of the sample components. In oneembodiment, the outer cover 28 is made of a flexible film which isstretched under pressure to contact the sonic member 76 during lysing toallow transmission of the sonic energy into the processing region 30.

The cover 28 in one embodiment is a flexible film of polymeric materialsuch as polypropylene, polyethylene, polyester, or other polymers. Thefilm may either be layered, e.g., laminates, or the films may behomogeneous. Layered films are preferred because they generally havebetter strength and structural integrity than homogeneous films. Inparticular, layered polypropylene films are presently preferred becausepolypropylene is not inhibitory to polymerase chain reaction (PCR).Alternatively, the cover 28 may comprise other materials such as a rigidpiece of plastic. In one preferred embodiment, the cover 28 is aninterface wall which is dome-shaped or includes stiffening ribs asshown, for example, in PCT Publication WO 00/73413 entitled “Apparatusand Method for Cell Disruption,” or commonly assigned, copending U.S.patent application Ser. No. 09/972,221, entitled “Apparatus and Methodfor Rapid Disruption of Cells or Viruses,” filed Oct. 4, 2001, theentire disclosures of which are incorporated herein by reference.

In general, the energy transmitting member that is operatively coupledto the processing region 30 for transmitting energy thereto may be anultrasonic, piezoelectric, magnetostrictive, or electrostatictransducer. The energy transmitting member may also be anelectromagnetic device having a wound coil, such as a voice coil motoror a solenoid device. It is presently preferred that the energytransmitting member be a sonic member, such as an ultrasonic horn.Suitable horns are commercially available from Sonics & Materials, Inc.having an office at 53 Church Hill, Newton, Conn. 06470-1614, U.S.A.Alternatively, the sonic member may comprise a piezoelectric disk or anyother type of ultrasonic transducer that may be coupled to the cover 28.In alternative embodiments, the energy transmitting member may be athermal element (e.g., a heater) for transmitting thermal energy to theprocessing region 30 or an electrical element for transmittingelectrical energy to the processing region 30. In addition, multipleenergy transmitting members may be employed simultaneously, e.g.,simultaneously heating and sonicating the processing region to effectlysis of cells, spores, viruses, or microorganisms trapped in theprocessing region.

In FIGS. 9H and 9HH, the valve 16 is rotated to place the secondexternal port 46 in fluidic communication with a mastermix or reagentchamber 78, and the piston 54 is pushed downward to elute the mixturefrom the processing region 30 to the reagent chamber 78. The reagentchamber 78 typically contains reagents (e.g., nucleic acid amplificationreagents and probes) to be mixed with the sample. Any excess mixture isdispensed into the waste chamber 64 via the second external port 46after rotating the valve 16 to place the port 46 in fluidiccommunication with the waste chamber 64, as shown in FIGS. 9I and 9II.The mixture is then mixed in the reagent chamber 78 by toggling. This iscarried out by placing the fluid displacement region 50 in fluidiccommunication with the reagent chamber 78 as shown in FIGS. 9J and 9JJ,and moving the piston 54 up and down. Toggling of the mixture throughthe filter in the processing region 30, for instance, allows largerparticles trapped in the filter to temporarily move out of the way topermit smaller particles to pass through. The reagent chamber 78 maycontain dried or lyophilized reagents that are reconstituted when mixedwith fluid.

In FIGS. 9K, 9KK, and 9K′K′, the valve 16 is rotated to place the firstexternal port 42 in fluidic communication with a first branch 84 coupledto the reaction vessel 18, while the second branch 86 which is coupledto the reaction vessel 18 is placed in fluidic communication with thecrossover groove 56. The first branch 84 and second branch 86 aredisposed at different radii from the axis 52 of the valve 16, with thefirst branch 84 having a common radius with the first external port 42and the second branch 86 having a common radius with the crossovergroove 56. The crossover groove 56 is also in fluidic communication withthe reagent chamber 78 (FIG. 9K), and serves to bridge the gap betweenthe reagent chamber 78 and the second branch 86 to provide crossoverflow therebetween. The external ports are disposed within a range ofexternal port radii from the axis and the crossover groove is disposedwithin a range of crossover groove radii from the axis, where the rangeof external port radii and the range of crossover groove radii arenon-overlapping. Placing the crossover groove 56 at a different radiusfrom the radius of the external ports 42, 46 is advantageous because itavoids cross-contamination of the crossover groove 56 by contaminantsthat may be present in the area near the surfaces between the valve 16and the housing 12 at the radius of the external ports 42, 46 as aresult of rotational movement of the valve 16. Thus, while otherconfigurations of the crossover groove may be used including those thatoverlap with the radius of the external ports 42, 46, the embodiment asshown is a preferred arrangement that isolates the crossover groove 56from contamination from the area near the surfaces between the valve 16and the housing 12 at the radius of the external ports 42, 46.

To fill the reaction vessel 18, the piston 54 is pulled upward to drawthe mixture in the reagent chamber 78 through the crossover groove 56and the second branch 86 into the reaction vessel 18. In such anarrangement, the reaction vessel 18 is the aspiration chamber orreferred to as the first chamber, and the reagent chamber 78 is thesource chamber or referred to as the second chamber. The valve 16 isthen rotated to place the second external port 46 in fluidiccommunication with the first branch 84 and to close the first externalport 42, as shown in FIGS. 9L and 9LL. The piston 54 is pushed downwardto pressurize the mixture inside the reaction vessel 18. The reactionvessel 18 may be inserted into a thermal reaction chamber for performingnucleic acid amplification and/or detection. The two branches 84, 86allow filling and evacuation of the reaction chamber of the reactionvessel 18. The vessel maybe connected to the housing 12 by ultrasonicwelding, mechanical coupling, or the like, or be integrally formed withthe housing 12 such as by molding. The use of a reaction vessel foranalyzing a fluid sample is described in commonly assigned, copendingU.S. patent application Ser. No. 09/584,328, entitled “Cartridge forConducting a Chemical Reaction,” filed May 30, 2000.

To operate the valve 16 of FIGS. 3-8, a motor such as a stepper motor istypically coupled to the toothed periphery 29 of the disk portion 22 torotate the valve 16 relative to the housing 12 for distributing fluidwith high precision. The motor can be computer-controlled according tothe desired protocol. A linear motor or the like is typically used todrive the piston 54 up and down with precision to provide accuratemetering, and may also be computer-controlled according to the desiredprotocol.

FIG. 10 shows another valve 100 which is rotatably coupled to a fluidcontrol channel housing or block 102. A reaction vessel 104 isdetachably coupled to the housing 102. The valve 100 is a generallytubular member with a longitudinal axis 105 as shown in FIG. 11. Apiston 106 is movably connected to the valve 100 to change the volume ofthe fluid displacement region 108 as the piston 106 is moved up anddown. A cover 109 is placed near the bottom of the valve 100. A fluidprocessing region 110 is disposed in the valve 100 and is in continuousfluidic communication with the fluid displacement region 108. The valve100 includes a pair of apertures serving as a first port 111 and asecond port 112, as best seen in FIG. 11. In the embodiment shown, theports 111, 112 are angularly spaced by about 120°, but the spacing maybe different in alternate embodiments. A crossover channel or groove 114is formed on the external surface 116 of the valve 100 and extendsgenerally in the longitudinal direction, as seen in FIG. 10. The twoports 111, 112 are disposed at different levels longitudinally offsetfrom one another along the longitudinal axis 105, and the crossovergroove 114 extends in the longitudinal direction of the axis 105bridging the two levels of the ports 111, 112.

The housing 102 has an opening 118 for receiving the portion of thevalve 100 having the ports 111, 112 and groove 114. The internal surface120 around the opening 118 is shaped to cooperate with the externalsurface 116 of the valve 100. Although a gasket may be placed betweenthe internal surface 120 and the external surface 116, a preferredembodiment employs tapered or conical surfaces 120, 116 that produce asealing effect without the use of an additional gasket. The housing 102includes a plurality of channels and ports and the valve 100 isrotatable around its axis 105 to allow the ports 111, 112 to be placedselectively in fluidic communication with the plurality of channels inthe housing 102. Depending on which port is opened or closed and whetherthe piston 106 is moved upward or downward, the fluid flow in the valve100 can change directions, and the ports 111, 112 can each switch frombeing an inlet port to an outlet port.

To demonstrate the fluid metering and distribution function of the valve100, FIGS. 12A-12N illustrate the operation of the valve 100 for aspecific protocol. As shown in FIG. 12A, the housing 102 includes aplurality of fluid channels. For convenience, the channels are labeledas follows: reagent channel 130, lysing channel 132, sample channel 134,wash channel 136, waste channel 138, first branch 140, and second branch142. The channels 130-138 extend from the internal surface 120 to oneexternal surface 144 which is generally planar, and the branches 140,142 extend from the internal surface 120 to another external surface 146which is also generally planar (FIG. 10). When assembled, the first port111 and the channels 130-134 lie on a first transverse plane that isperpendicular to the longitudinal axis 105, while the second port 112,the channels 136, 138, and the two branches 140, 142 lie on a secondtransverse plane that is perpendicular to the longitudinal axis 105. Thesecond transverse plane is longitudinally offset from the firsttransverse plane. For convenience, the second port 112, the channels136, 138, and the branches 140, 142 are shaded to indicate that they arelongitudinally offset from the first port 111 and the channels 130-134.The crossover groove 114 extends longitudinally to bridge the offsetbetween the first and second transverse planes. A chamber body 150 isconnected to the housing 102 (FIG. 10), and includes the reagentchamber, lysis chamber, sample chamber, wash chamber, and waste chamberthat are respectively coupled fluidicly with the channels 130-138. Thefirst and second branches 140, 142 are fluidicly coupled with thereaction vessel 104.

In FIG. 12A, the first port 111 is placed in fluidic communication withthe sample channel 134 and the piston 106 is pulled upward to draw afluid sample into the fluid displacement region 108 (FIG. 11). The valve100 is then rotated to place the second port 112 in fluidiccommunication with the waste channel 138 and the piston 106 is pusheddownward to drive the fluid sample from the displacement region 108through the processing region 110, and out through the waste channel138, as shown in FIG. 12B. These steps are typically repeated until anentire sample is processed through the processing region 110, forinstance, to capture sample components on a trapping member such as afilter.

In FIG. 12C, the valve 100 is rotated to place the second port 112 influidic communication with the wash channel 136 to aspirate a wash fluidinto the processing region 110 by pulling the piston 106 upward. Thevalve 100 is then rotated to place the second port 112 in fluidiccommunication with the waste channel 138 and the piston 106 is pusheddownward to drive the wash fluid from the processing region 110 outthrough the waste channel 138. The above washing steps can be repeatedas desired to remove unwanted residue inside the valve 100.

For lysing, the valve 100 is rotated to place the first port 111 influidic communication with the lysing channel 132 and the piston 106 ispulled upward to draw a lysing fluid into the fluid displacement region108, as shown in FIG. 12E. In FIG. 12F, the valve 110 is rotated toclose both ports 111, 112. The piston 106 is pushed downward to push thelysing fluid into the processing region 110 and to pressurize the lysingfluid and the sample components captured in the fluid processing region110. Additional energy may be applied to the mixture in the processingregion 110 including, for instance, sonic energy transmitted into theprocessing region 110 by operatively coupling a sonic member with thecover 109 (FIG. 11).

In FIG. 12G, a desired preset amount of wash fluid is aspirated into theprocessing region 110 from the wash channel 136 through the second port112 to dilute the mixture. The valve 100 is then rotated to place thefirst port 111 in fluidic communication with the reagent channel 130 todischarge a preset amount of the mixture from the processing region 110to the reagent chamber, as shown in FIG. 12H. The piston 106 is moved upand down to agitate and mix the mixture by toggling. The balance of themixture is discharged through the second port 112 to the waste channel138, as shown in FIG. 12I. Another wash is performed by drawing a washfluid from the wash channel 136 through the second port 112 into theprocessing region 110 (FIG. 12J), and discharging the wash fluid fromthe processing region 110 through the second port 112 to the wastechannel 138 (FIG. 12K).

In FIG. 12L, the valve 100 is rotated to place the second port 112 influidic communication with the first branch 140 coupled to the reactionvessel 104, while the second branch 142 which is coupled to the reactionvessel 104 is placed in fluidic communication with the crossover groove114. The second branch 142 is longitudinal offset from the reagentchannel 130. In the position as shown in FIG. 12L, the crossover groove114 extends longitudinally to bridge the offset between the secondbranch 142 and the reagent channel 130 to place them in fluidiccommunication with one another. As a result, the fluid processing region110 is in fluidic communication, through the first branch 140, thereaction vessel 104, the second branch 142, and the crossover groove114, with the reagent channel 130.

By pulling the piston 106 upward, the mixture in the reagent chamber isdrawn from the reagent channel 130 through the crossover groove 114 andthe second branch 142 into the reaction vessel 104. The valve 100 isthen rotated to place the second port 112 in fluidic communication withthe second branch 142 and to close the first port 111, as shown in FIG.12M. The piston 106 is pushed downward to pressurize the mixture insidethe reaction vessel 104. In FIG. 12N, the valve 100 is rotated to closethe ports 111, 112 and isolate the reaction vessel 104. The reactionvessel 104 may be inserted into a thermal reaction chamber forperforming nucleic acid amplification and/or detection.

As illustrated in the above embodiments, the fluid control andprocessing system is advantageously a fully contained system that isversatile and adaptable. The fluid displacement region is the motivatingforce for moving fluid in the system. By maintaining a continuousfluidic communication between the fluid displacement region and thefluid processing region, the motivating force for moving fluid in thesystem is fluidicly coupled to the processing region at all times. Thefluid displacement region (motivating force) also acts as a temporarystorage area for the fluid being driven through the system. While theembodiments shown employ a moving piston in the fluid displacementregion as the motivating force, other mechanisms may be used including,e.g., pneumatic pump mechanisms or the like which use pressure as themotivating force without a change in volume of the fluid displacementregion. The inlet or outlet side of the fluid processing region canaddress any of the chambers to permit random access to reagents andother fluids. Complex protocols can be programmed relatively easily intoa computer controller and then executed using the versatile fluidcontrol and processing system. A myriad of different protocols can beperformed using a single platform.

In the embodiments shown, the fluid control occurs by addressing a pairof ports in the valve to place only one port at a time selectively influidic communication with the chambers. This is accomplished by keepingthe pair of ports out of phase relative to the chambers. A crossover orbypass channel provides additional fluid control capability (e.g.,allowing convenient filling and emptying of the reaction vessel withinthe closed system). Of course, different porting schemes may be used toachieve the desired fluid control in other embodiments. Moreover, whilethe embodiments shown each include a single fluid processing region inthe valve body, additional processing regions can be located in thevalve body if desired. Generally, the valve body needs (n+1) ports per nprocessing regions.

The use of a single valve produces high manufacturing yields due to thepresence of only one failure element. The concentration of the fluidcontrol and processing components results in a compact apparatus (e.g.,in the form of a small cartridge) and facilitates automated molding andassembly. As discussed above, the system advantageously includesdilution and mixing capability, intermediate wash capability, andpositive pressurization capability. The fluid paths inside the systemare normally closed to minimize contamination and facilitate containmentand control of fluids within the system. The reaction vessel isconveniently detachable and replaceable, and may be disposable in someembodiments.

The components of the fluid control and processing system may be made ofa variety of materials that are compatible with the fluids being used.Examples of suitable materials include polymeric materials such aspolypropylene, polyethylene, polycarbonate, acrylic, or nylon. Thevarious chambers, channels, ports, and the like in the system may havevarious shapes and sizes.

The above-described arrangements of apparatus and methods are merelyillustrative of applications of the principles of this invention andmany other embodiments and modifications may be made without departingfrom the spirit and scope of the invention as defined in the claims.

For instance, FIG. 13 shows a soft-walled chamber 200 that may beincorporated into the fluid control and processing system. Typically, anon-board reagent style cartridge requires a total fluid volume of atleast twice the total volume of reagents and sample combined in rigidsystems. The use of soft-walled chambers can reduce the required volume.These chambers have flexible walls, and can typically be formed usingfilms and thermoforming. An added advantage of soft walls is thatventing need not be provided if the walls are sufficiently flexible toallow them to collapse when the chamber is emptied. In FIG. 13, aflexible sidewall 202 separates a reagent chamber 204 and a wastechamber 206. Because the waste is composed of the sample and reagents,the volume required for waste is no more than the sum of the sample andreagents. The reagent chamber 204 contracts while the waste chamber 206expands, and vice versa. This can be a closed system with no connectionto the exterior. The configuration can reduce the overall size of thecartridge, and can allow fast change-overs of chamber volumes. It canalso eliminate venting, and can cut costs by reducing the number ofplatforms that would otherwise need to be built with hard tooling. Inone embodiment, at least two of the plurality of chambers in the systemare separated by a flexible wall to permit change-over of chambervolumes between the chambers.

FIG. 14 shows a piston assembly 210 including a piston rod 212 connectedto a piston shaft 214 having a smaller cross-section than the rod 212for driving small amounts of fluids. The thin piston shaft 214 may bendunder an applied force if it is too long. The piston rod 212 moves alongthe upper portion of the barrel or housing 216, while the piston shaft214 moves along the lower portion of the barrel 216. The movement of thepiston rod 212 guides the movement of the piston shaft 214, and absorbsmuch of the applied force so that very little bending force istransmitted to the thin piston shaft 214.

FIG. 15 shows a side chamber 220 that may be incorporated into thesystem. The side chamber 220 includes an inlet port 222 and an outletport 224. In this example, the side chamber 220 includes a filter 226disposed at the inlet port 222. Fluid is directed to flow via the inletport 222 into the side chamber 220 and out via the outlet port 224 forside filtering. This allows filtering of a fluid sample or the likeusing the fluid control system of the invention. The fluid may berecirculated to achieve better filtering by the filter 226. Thisprefiltering is useful to remove particles before introducing the fluidinto the main chambers of the system to prevent clogging. The use of aside chamber is advantageous, for instance, to avoid contaminating thevalve and the main chambers in the system.

A fluid sample may be introduced into the housing 12 of the fluidcontrol and processing system 10, which may be configured as acartridge, by a variety of mechanisms, manual or automated. For manualaddition, a measured volume of material may be placed into a receivingarea of the housing 12 (e.g., one of the plurality of chambers) throughan input port and a cap is then placed over the port. Alternatively, thereceiving area may be covered by a rubber or similar barrier and thesample is injected into the receiving area by puncturing the barrierwith a needle and injecting the sample through the needle.Alternatively, a greater amount of sample material than required for theanalysis can be added to the housing 12 and mechanisms within thehousing 12 can effect the precise measuring and aliquoting of the sampleneeded for the specified protocol.

It may be desirable to place certain samples, such as tissue biopsymaterial, soil, feces, exudates, and other complex material into anotherdevice or accessory and then place the secondary device or accessoryinto the housing causing a mechanical action which effects a functionsuch as mixing, dividing, or extraction. For example, a piece of tissuemay be placed into the lumen of a secondary device that serves as theinput port cap. When the cap is pressed into the port, the tissue isforced through a mesh that slices or otherwise divides the tissue.

For automated sample introduction, additional housing or cartridgedesign features are employed and, in many cases, impart samplecollection functionality directly into the housing. With certainsamples, such as those presenting a risk of hazard to the operator orthe environment, such as human retrovirus pathogens, the transfer of thesample to the housing may pose a risk. Thus, in one embodiment, asyringe or sipper may be integrated into the device to provide a meansfor moving a sample directly into the housing. Alternatively, the devicemay include a venous puncture needle and a tube forming an assembly thatcan be used to acquire a sample. After collection, the tube and needleare removed and discarded, and the housing 12 is then placed in aninstrument to effect processing. The advantage of such an approach isthat the operator or the environment is not exposed to pathogens.

The input port can be designed with a consideration of appropriate humanfactors as a function of the nature of the intended specimen. Forexample, respiratory specimens may be acquired from the lowerrespiratory tract as expectorants from coughing, or as swab or brushsamples from the back of the throat or the nares. In the former case,the input port can be designed to allow the patient to cough directlyinto the housing 12 or to otherwise facilitate spitting of theexpectorated sample into the housing. For brush or swab specimens, thespecimen is placed into the input port where features of the port andclosure facilitate the breaking off and retaining of the end of the swabor brush in the cartridge receiving area.

In another embodiment, the housing 12 includes one or more input tubesor sippers that may be positioned in a sample pool so that the samplematerial flows into the housing 12. Alternatively, a hydrophilic wickingmaterial can function to draw a sample into the device. For example, theentire cartridge can be immersed directly into the sample, and asufficient amount of sample is absorbed into the wicking material andwicks into the housing 12. The housing is then removed, and can betransported to the laboratory or analyzed directly using a portableinstrument. In another embodiment, tubing can be utilized so that oneend of the tube is in direct communication with the housing to provide afluidic interface with at least one chamber and the other end isaccessible to the external environment to serve as a receiver forsample. The tube can then be placed into a sample and serve as a sipper.Thus, the device may include a variety of features for collecting asample from various different sources and for moving the sample into thehousing 12, thereby reducing handling and inconvenience.

FIG. 16 shows a fluid control and processing system 310 including ahousing 312 having a plurality of chambers 313 wherein one of thechambers is a processing chamber 314. The housing 312 includes aplurality of chamber ports 325 configured to communicate with a fluidcontrol device such as a rotary fluid control valve similar to therotary valve 16 in the system 10 of FIGS. 1-4. The valve has a fluiddisplacement region similar to the fluid displacement region 50 in thesystem 10. The chambers 313 may include the same chambers as in theembodiment of FIGS. 1-4 (i.e., sample chamber 60, waste chamber 64, washchamber 66, lysis chamber 70, reagent chamber 78, and reaction vessel18). The housing 312 also includes a fluid processing region or activeregion similar to the fluid processing region 30 of system 10 in FIGS.1-4. In such a configuration, the chamber ports 325 will face theexternal port surface of the disk portion of a rotary fluid controlvalve

The processing chamber 314 has a first port 326 and a second port 327.In one example, the first port 326 may be an inlet port for taking influid, and the second port 327 may be an outlet port for dischargingfluid from the processing chamber 314. The processing chamber 314typically is integrally formed or built into the main body of thehousing 312, so that the inlet and outlet ports of the processingchamber are two of the chamber ports. Alternatively, the processingchamber 314 may be formed as a separate member that can be inserted intothe main body of the housing 312, the inserted member having inlet andoutlet ports that align with two of the chamber ports.

The processing chamber 314 may contain a processing chamber material,such as an enrichment material or medium or a depletion material ormedium. An enrichment material captures a target such as an analyte fromthe fluid that passes through the processing chamber 314. A depletionmaterial traps or retains unwanted material from the fluid that passesthrough the processing chamber 314. The enrichment or depletion materialmay comprise one or more solid phase materials. In general, the solidphase materials may include beads, fibers, membranes, filter paper,glass wool, polymers, and gels.

For example, enrichment materials may include chromatographic materials,more particularly absorptive phase materials, such as reverse phasematerials, ion-exchange materials, or affinity chromatographic materialsin which a binding member is covalently bound to an insoluble matrix.For the affinity chromatographic materials, the binding member may begroup specific (e.g., a lectin, enzyme cofactor, Protein A and the like)or substance specific (e.g., antibody or binding fragment thereof,antigen for a particular antibody of interest, oligonucleotide and thelike). The insoluble matrix to which the binding member is bound may beparticles, such as porous glass or polymeric beads, networks of glassstrands or filaments, a plurality of narrow rods or capillaries, and thelike. For example, the insoluble matrix may include beads functionalizedwith antibodies for capturing antigens or haptens for an immunoassayprocedure.

Instead of coated particles or other insoluble matrices, one may employa coated/impregnated membrane which provides for selective retention ofthe analyte comprising fraction of a fluid sample while allowing theremainder of the sample to flow through the membrane and out of theprocessing chamber. A variety of hydrophilic, hydrophobic, andion-exchange membranes have been developed for solid phase extraction.

Another example of an enrichment material is a gel medium, which can beused to provide for a diversity of different sieving capabilities. Theenrichment channel through the processing chamber 314 serves to enrich aparticular analyte comprising fraction of a liquid sample. By varyingthe pore size of the media, employing two or more gel media of differentporosity, and/or providing for a pore size gradient, one can ensure thatthe analyte comprising fraction of interest of the initial sample isretained in the gel medium.

For some enrichment materials or depletion materials, it may benecessary to employ a retention mechanism to keep the particularmaterial in the processing chamber. Frits such as glass frits may beused to retain the material in the processing chamber. FIGS. 18-23 showtwo frits 330, 332 disposed inside the processing chamber 314. In theembodiment shown, the frits 330, 332 are held in place by a retainingstructure or member 336. The retaining member 336 may be configured as aprocessing module or an insert that can be easily snapped into place ina receiving area of the processing chamber 314 and can be convenientlyremoved as desired. As shown in FIG. 17, in a specific embodiment, theprocessing chamber 314 includes a receiving area 329 for receiving aprocessing module containing an enrichment material or a depletionmaterial. In other embodiments, the processing module may comprise acolumn containing a separation material or a structure containing aseparation channel for capillary electrophoresis or isoelectricfocusing. The processing chamber 314 has a collection area 331 forreceiving fluid that has flowed through the processing module 336.

Referring to FIGS. 18-23, the processing module 336 preferably includesa spout 333 that directs the fluid into the collection area 331. Theprocessing module includes a first frit 330 that is disposed adjacentthe first port 326, and the second frit 332 is spaced from the firstfrit 330 to provide a space 338 for the enrichment material or depletionmaterial. In one embodiment, the fluid enters the processing chamber 314through the first port 326, passes through the first frit 330, theenrichment material or depletion material in the space 338, and thesecond frit 332, and then by gravity flows to the collection area 331 ofthe processing chamber above the second port 327 and exits theprocessing chamber 314 through the port 327. The space 338 serves asanother fluid processing region.

In one example, a sample fluid is drawn from the sample chamber byrotating the valve to place the fluid displacement region in fluidiccommunication with the sample chamber via the first external port. Thisis illustrated for the system 10 of FIGS. 1-4 in FIGS. 9A and 9AA, whichis generally the same as the system 310 of FIGS. 16-23 except for theadditional processing chamber 314 in the system 310. The sample fluidbypasses the fluid processing region (region 30 in system 10), andenters the fluid displacement region (region 50 in system 10). The valve(valve 16 in system 10) is rotated to place the first external port influidic communication with the processing chamber 314. The sample fluidis driven from the fluid displacement region into the processing chamber314 via the inlet port 326, bypassing the fluid processing region. Asthe fluid flows through the processing chamber 314 containing anenrichment material via the inlet port 326, for example, the analytecomprising sample fraction will be retained by the enrichment materialsuch as a chromatographic material in the processing chamber 314. Theremaining waste portion of the fluid is drawn out of the processingchamber 314 through the outlet port 327 and into the fluid displacementregion of the valve by rotating the valve to place the first externalport in fluidic communication with the outlet port 327 of the processingchamber 314. The valve is then rotated to place the first external portin fluidic communication with the waste chamber (chamber 64 in system10), and the waste fluid is driven from the fluid displacement regioninto the waste chamber. An elution liquid may then flow through theenrichment material in the processing chamber 314 to release theenriched sample fraction from the enrichment material and carry it fromthe processing chamber 314 to another chamber or another region such asan active region. The elution liquid may be first drawn into the fluiddisplacement region of the valve from another chamber, and then drivenfrom the fluid displacement region into the inlet port 326 of theprocessing chamber 314 by manipulating the rotary valve. The elutionliquid and the released enriched sample fraction may be drawn from theprocessing chamber 314 via the outlet port 327, either into the fluiddisplacement region through the first external port (port 42 in system10) bypassing the fluid processing region, or through the fluidprocessing region (region 30 in system 10) and into the fluiddisplacement region through the second external port (port 46 in system10). The rotary valve may be further manipulated to transfer the fluidto other chambers or regions of the system 310.

In another example a depletion material is provided in the processingchamber 314 for trapping or removing unwanted material from a samplefluid. The valve can be used to transfer the sample fluid from thesample chamber to the processing chamber 314 as described above. As thefluid flows through the processing chamber 314 containing a depletionmaterial via the inlet port 326, the unwanted materials such as cellulardebris, contaminants, or amplification inhibitors are depleted from thefluid. The remaining fluid is drawn out of the processing chamber 314through the outlet port 327 by rotating the valve to place the fluiddisplacement region in fluidic communication with the outlet port 327.The fluid may be drawn through the second external port (port 46 insystem 10) first into the fluid processing region (region 30 in system10) and then into the fluid displacement region of the valve.Alternatively, the fluid may be drawn through the first external port(port 42 in system 10) into the fluid displacement region bypassing thefluid processing region. The fluid may subsequently be driven from thefluid displacement region into another chamber or region of the system310 by manipulating the rotary valve.

Instead of solid phase materials, the processing chamber 314 may houseliquid phase materials such as, for example, ficoll, dextran,polyethylene glycol (PEG), sucrose, and the like.

By providing one or more processing chambers in the fluid processingsystem 310, the system 310 becomes more versatile, and is capable ofperforming additional steps of sample preparation other than thoseperformed in the active region or processing region in the valve body(e.g., processing region 30 in FIG. 8), to achieve multi-stagedfiltration, consecutive functions, and the like in a single device.Moreover, the processing chamber may be fluidicly coupled with anexternal fluid volume to facilitate large volume processing. Theprocessing chamber may also be fluidicly coupled with an externalchamber that contains materials that are not desirable inside the mainbody 312 of the fluid processing system 310.

In general, the processing regions in the processing chambers (e.g.,processing chamber 314 in FIG. 16) and in the valve body (e.g.,processing region 30 in FIG. 8) may each contain enrichment materials ordepletion materials. In some embodiments, each processing region maycontain one or more such materials. For example, a filter (e.g., thefilter or filter stack 27 in FIG. 8) or beads may be placed in aprocessing region to remove unwanted materials such as cellular debrisfrom the sample or for accomplishing concentration of cells. The filteror beads may be used to bind specific targets such as particularmolecules in the sample, or to remove specific targets such as proteins,inhibitors, or the like. In some embodiments, a processing regionincludes a filter and another solid phase material such as beads,fibers, or wool, for molecular isolation of molecular targets ormolecular removal of molecular materials. In other embodiments, aprocessing region may include different types of beads such as magneticbeads, glass beads, polymeric beads, and the like. The beads can be usedfor cell capture, cell lysis, binding of analyte, binding of unwantedmaterial, or the like. In some embodiments, a single type of beads maybe used to perform two or more of the functions of cell capture, celllysis, binding of analyte, and binding of unwanted material. Forinstance, cells can be adhered to the beads and lysed to release theirnucleic acid content, and the lysate together with the released nucleicacid can be moved to a separate region or chamber for furtherprocessing, leaving behind the beads and their adherent cellular debris.

In another embodiment, a separation channel is provided for performingcapillary electrophoresis (CE), isoelectric focusing (IEF), or the like.This may be done before or after nucleic acid amplification. Theseparation channel may be a separate member that is inserted into achamber of the fluid processing system, may be formed as a microchannelin the housing of the system, or may be built into one of the chambersof the system.

FIG. 24 shows a separation channel or region 350 in the fluid controland processing system 354. The separation channel 350 is typicallyformed as a separate member that is assembled into the system 354 andmay in some embodiments be disposed in a chamber 352. Alternatively, theseparation channel 350 may be integrally formed or built into the system354. The separation channel 350 may be a thin channel or a capillarycoupled between at least two electrodes, which in the specificembodiment shown include two metal tubes 356, 358. The lower end of thechannel 350 is fluidicly coupled to a lower reservoir 361 which isfluidicly coupled to a chamber port or reservoir port 360, while theupper end of the channel 350 is fluidicly coupled to a vented reservoir362 provided in a support structure 366 for supporting the separationchannel 350. The metal tubes 356, 358 serve as electrodes to receiveelectrical energy and apply an electric field to the fluid in theseparation channel 350. Conductive wires in contact with the metal tubes356, 358 may be molded into plastic and lead to respective contact areason the external surface of the housing of the system 354. A voltagesource may then be connected to the contact areas to apply a voltagedifference between the contact areas and thus between the electrodes.Alternatively, electrodes may be provided as part of an externalinstrument for applying the electric field, and be dipped intoreservoirs at the ends of the separation channel 350. The sample fluidis typically pumped by the piston 368 of the valve 370 from the fluiddisplacement region 372 through one of the external ports of the valvebody (e.g., the external port 342) to the separation channel 350 via thereservoir port 360 and reservoir 361. A sample plug is injected into theseparation channel 350, and the remaining portion of the sample fluid inthe reservoir 361 may then be drawn via the chamber port 360 into thefluid displacement region 372 of the valve 370 by the piston 368. Thereservoir 362 may be used to introduce buffer, elution solvent, reagent,rinse and wash solutions, or the like into the electrophoretic flow pathof the separation channel 350.

Entities in the sample plug, such as molecules, particles, cells, andthe like are moved through a medium contained in the separation channel350 under the influence of the applied electric field. Depending on thenature of the entities (e.g., whether they carry an electrical charge),as well as the surface chemistry of the electrophoretic chamber in whichthe electrophoresis is carried out, the entities may be moved throughthe medium under the direct influence of the applied electric field oras a result of bulk fluid flow through the pathway resulting from theapplication of the electric field such as an electroosmotic flow. As thesample plug separates into species bands in the separation channel 350,the bands are detected, for instance, optically by a single pointdetector disposed at a fixed location or by a scanning detector thatscans along the length of the channel 350. To facilitate opticaldetection, a portion of the housing may be optically transmissive ortransparent. Alternatively, the detector may be inserted into thehousing and placed adjacent the channel 350 (e.g., in a chamber whichhouses the channel 350).

Typically, separation is performed after amplification, for instance,using the method as described above in FIGS. 9A-9LL. In one example, anamplified product (e.g., nucleic acid amplified by PCR) is introduced asthe sample into the reservoir 361. The separation channel 350 isprefilled with a separation material such a gel or buffer. A voltage isapplied via the electrodes 356, 358 to inject a sample plug from thereservoir 361. The rest of the sample is then removed from the reservoir361. Next, a buffer such as an electrolyte solution is introduced intothe reservoir 361. A voltage difference is applied between theelectrodes 356, 358 to form an electric field that induces flow of asample plug through the separation channel 350 and separates the sampleplug therein into species bands, which are detected using, for instance,a single-point optical detector or a scanning detector.

FIG. 25 shows the valve 416 of another system 410 which has a housingwith a plurality of chambers similar to the system 10 of FIGS. 1-4,except that the valve 416 has only one external port 442. The valve 416includes a valve body 420 having a disk portion 422 and a tubularportion 424. The disk portion 422 has a generally planar external portsurface 423. The valve 416 is rotatable relative to the housing 412 ofthe system 410 (see FIGS. 26A and 26AA). The housing 412 includes aplurality of chamber ports facing the external port surface 423 of thedisk portion 422 of the valve 416 to permit fluidic communicationbetween the chambers of the housing 412 and the valve 416. The diskportion 422 includes a fluid processing region 430, a first flow channel440 extending between the external port 442 and the fluid processingregion 430, and a second flow channel 438 extending between the fluidprocessing region 430 and a fluid displacement region 450 in the tubularportion 424 of the valve 416. The fluid processing region 430 is incontinuous fluidic communication with the fluid displacement region 450.An outer cover 428 is placed over the fluid processing region 430. Thefluid processing region 430 may be used to subject a fluid flowingtherethrough to various acoustical, optical, thermal, electrical,mechanical, or chemical processing.

As shown in FIG. 25, a fluid displacement member in the form of aplunger or piston 454 is movably disposed in the displacement region 450of the tubular portion 424 to move up and down along the axis 452. Whenthe piston 454 moves upward, it expands the volume of the displacementregion 450 to produce a suction for drawing fluid into the region 450.When the piston 454 moves downward, it decreases the volume of thedisplacement region 450 to drive fluid out of the region 450. As therotary valve 416 is rotated around its axis 452 relative to the housing412, the external port 442 may be fluidicly coupled with one of thechambers or reaction vessel in the housing 412. Depending on the actionof the piston 454, the external port 442 is either an inlet port or anoutlet port.

To demonstrate the fluid metering and distribution function of the valve416, FIGS. 26A-26EE illustrate the operation of the valve 416 for aspecific protocol. In FIGS. 26A and 26AA, the external port 442 isplaced in fluidic communication with a sample chamber 460 by rotatingthe valve 416, and the piston 454 is pulled upward to draw a fluidsample from the sample chamber 460 through the first flow channel 440,the fluid processing region 430, and the second flow channel 438 andinto the fluid displacement region 450. For simplicity, the piston 454is not shown in FIGS. 26A-26EE.

As shown in FIGS. 26B and 26BB, the valve 416 is then rotated to placethe external port 442 in fluidic communication with a storage chamber470 which contains a lysing fluid (e.g., a lysing reagent or buffer).The piston 454 is pushed downward to transfer the fluid sample from thefluid displacement region 450 to the storage chamber 470. The piston 454is then pulled upward to draw the fluid sample and lysing fluid from thestorage chamber 470 to the fluid displacement region 450. The lysingfluid mixes with the sample and effects lysis of cell or viruses in thesample. Additional energy may be applied to the processing region 430 toassist the lysing process. For instance, a sonic member 476 such as anultrasonic horn may be placed in contact with the outer cover 428 totransmit ultrasonic energy into the processing region 430 to facilitatelysing of cells or viruses of the fluid sample as the fluid flows fromthe fluid displacement region 450 to the storage chamber 470 and/or fromthe storage chamber 470 back to the fluid displacement region 450. Theouter cover 428 in one preferred embodiment is an interface wall whichis dome-shaped or includes stiffening ribs.

In FIGS. 26C and 26CC, the valve 416 is rotated to place the externalport 442 in fluidic communication with a reagent chamber 478, and thepiston 454 is pushed downward to force the lysate to flow from the fluidprocessing region 430 to the reagent chamber 478. The reagent chamber478 typically contains reagents (e.g., PCR reagents and fluorescentprobes) to be mixed with the fluid sample. The fluids are then mixed inthe reagent chamber 478 by toggling the mixture between the fluiddisplacement region 450 and the reagent chamber 478 as the piston 454 ismoved up and down.

In FIGS. 26D, 26DD, and 26D′D′, the valve 416 is rotated to place theexternal port 442 in fluidic communication with a first branch 484coupled to the reaction vessel 418, while the second branch 486 which iscoupled to the reaction vessel 418 is placed in fluidic communicationwith the crossover groove 456. The first branch 484 and second branch486 are disposed at different radii from the axis 452 of the valve 416,with the first branch 484 having a common radius with the external port442 and the second branch 486 having a common radius with the crossovergroove 456. The crossover groove 456 is also in fluidic communicationwith the reagent chamber 478 (FIG. 26D), and serves to bridge the gapbetween the reagent chamber 478 and the second branch 486 to providecrossover flow therebetween. The external port is disposed within arange of external port radii from the axis and the crossover groove isdisposed within a range of crossover groove radii from the axis, wherethe range of external port radii and the range of crossover groove radiiare non-overlapping. Placing the crossover groove 456 at a differentradius from the radius of the external port 442 is advantageous becauseit avoids cross-contamination of the crossover groove 456 bycontaminants that may be present in the area near the surfaces betweenthe valve 416 and the housing 412 at the radius of the external port 442as a result of rotational movement of the valve 416.

To fill the reaction vessel 418, the piston 454 is pulled upward to drawthe mixture in the reagent chamber 478 through the crossover groove 456and the second branch 486 into the reaction vessel 418. In such anarrangement, the reaction vessel 418 is the aspiration chamber orreferred to as the first chamber, and the reagent chamber 478 is thesource chamber or referred to as the second chamber. The valve 416 isthen rotated to place the external port in fluidic communication withthe first branch 484, as shown in FIGS. 26E and 26EE. The piston 454 ispushed downward to pressurize the mixture inside the reaction vessel418. The reaction vessel 418 may be inserted into a thermal reactionchamber for performing nucleic acid amplification and/or detection. Thetwo branches 484, 486 allow filling and evacuation of the reactionchamber of the reaction vessel 418.

The fluid control and processing system 410 of FIGS. 26-26EE is modifiedfrom the system 10 of FIGS. 1-9LL to provide only one external port.Similarly, the valve 100 of FIGS. 10-12 may also be modified to provideonly one external port by removing one of the two external ports 111,112 and reconfiguring the fluid channels 130-138 and branches 140, 142between the valve 100 and the various chambers and reaction vessel 104.

The scope of the invention should, therefore, be determined not withreference to the above description, but instead should be determinedwith reference to the appended claims along with their full scope ofequivalents.

1-48. (canceled)
 49. A fluid control and processing system comprising: ahousing having a plurality of chambers and at least one separationchannel; and a valve body including a single fluid processing regioncontinuously coupled fluidicly with a single fluid displacement region,the fluid displacement region including or being connected to a meansthat depressurizes the fluid displacement region to draw fluid into thefluid displacement region and pressurizes the fluid displacement regionto expel fluid from the fluid displacement region, the valve bodyincluding at least one external port, the fluid processing region beingfluidicly coupled with the at least one external port, the fluiddisplacement region being fluidicly coupled with at least one externalport of the valve body, and the valve body being adjustable with respectto the housing to allow the at least one external port to be placedselectively in fluidic communication with the plurality of chambers andwith the at least one separation channel.
 50. The system of claim 49,further comprising a plurality of electrodes coupled to the housing toapply an electric field across at least a portion of the separationchannel.
 51. The system of claim 50, wherein the electrodes comprise apair of metal tubes at the two opposite ends of the separation channel.52. The system of claim 49, further comprising reservoirs fluidiclycoupled to opposite ends of the separation channel, and a reservoir portfluidicly coupled to one of the reservoirs for communicating with the atleast one external port of the valve body.
 53. The system of claim 49,wherein at least one of the chambers is a reagent chamber containingdried or lyophilized reagents.
 54. The system of claim 49, wherein thevalve body includes at least two external ports, which are disposed on agenerally planar external port surface of the valve body, and whereinthe valve body is rotatable around an axis and relative to the pluralityof chamber ports to allow the external ports to be placed selectively influidic communication with the plurality of chambers, the axis beingperpendicular to the external port surface, and the external ports beingspaced from the axis by a common radius.
 55. The system of claim 49,wherein the valve body is adjustable with respect to the housing toclose the external port so that the fluid displacement region and thefluid processing region are fluidicly isolated from the chambers. 56.The system of claim 49, wherein the fluid displacement region isdepressurizable by increasing in volume and is pressurizable bydecreasing in volume.
 57. The system of claim 56, further comprising afluid displacement member disposed in the fluid displacement region, thefluid displacement member being movable to adjust the volume of thefluid displacement region.
 58. The system of claim 57, wherein the fluiddisplacement member comprises a piston movable in a linear direction inthe fluid displacement region.
 59. The system of claim 58, wherein thefluid displacement member comprises a piston shaft which is connected toa distal portion of a piston rod for driving the piston shaft to moveinside the fluid displacement region, the piston shaft being smaller incross-section than the piston rod.
 60. The system of claim 49, furthercomprising an energy transmitting member operatively coupled with thefluid processing region for transmitting energy thereto to process fluidcontained therein.
 61. The system of claim 60, further comprising acover disposed between the fluid processing region and the energytransmitting member.
 62. The system of claim 61, wherein the covercomprises a rigid shell.
 63. The system of claim 60, wherein the energytransmitting member comprises an ultrasonic member for transmittingultrasonic energy through the cover into the fluid processing region.64. The system of claim 49, wherein the valve body includes a crossoverchannel, the valve body being adjustable with respect to the housing toplace the crossover channel in fluidic communication with an aspirationchamber and a source chamber to permit aspiration of a fluid from thesource chamber through the crossover channel to the aspiration chamber.65. The system of claim 64, wherein the valve body is rotatablyadjustable around an axis, and wherein the at least one external port isdisposed within a range of external port radii from the axis and thecrossover channel is disposed within a range of crossover channel radiifrom the axis, the range of external port radii and the range ofcrossover channel radii being non-overlapping.
 66. The system of claim65, wherein the crossover channel is a circular arc lying on a commoncrossover channel radius from the axis.
 67. The system of claim 49,wherein at least two of the plurality of chambers are separated by aflexible wall to permit change-over of chamber volumes between thechambers.